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5  structures 1533  species 0  interactions 3164  sequences 69  architectures

Family: Ufd2P_core (PF10408)

Summary: Ubiquitin elongating factor core

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Ubiquitin elongating factor core Provide feedback

This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, PF04564 which has ligase activity.

Literature references

  1. Tu D, Li W, Ye Y, Brunger AT; , Proc Natl Acad Sci U S A. 2007;104:15599-15606.: Inaugural Article: Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p. PUBMED:17890322 EPMC:17890322


This tab holds annotation information from the InterPro database.

InterPro entry IPR019474

This entry represents the most conserved part of the core region of ubiquitin conjugation factor E4 (or Ub elongating factor, or Ufd2P), running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C terminus, ( INTERPRO ), which has ligase activity.

Ubiquitin conjugation factor E4 is involved in N-terminal ubiquitin fusion degradation proteolytic pathway (UFD pathway). E4 binds to the ubiquitin moieties of preformed conjugates and catalyses ubiquitin chain assembly in conjunction with E1, E2, and E3. E4 appears to influence the formation and topology of the multi-Ub chain as it enhances ubiquitination at 'Lys-48' but not at 'Lys-29' of the N-terminal Ub moiety.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(153)
Full
(3164)
Representative proteomes UniProt
(5408)
RP15
(680)
RP35
(1468)
RP55
(2491)
RP75
(3272)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(153)
Full
(3164)
Representative proteomes UniProt
(5408)
RP15
(680)
RP35
(1468)
RP55
(2491)
RP75
(3272)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(153)
Full
(3164)
Representative proteomes UniProt
(5408)
RP15
(680)
RP35
(1468)
RP55
(2491)
RP75
(3272)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Wood V, Pfam-B_4085 (release 22.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Coggill P
Number in seed: 153
Number in full: 3164
Average length of the domain: 535 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 54.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 627
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ufd2P_core domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044QNP6 View 3D Structure Click here
A0A077ZD73 View 3D Structure Click here
A0A0A2V403 View 3D Structure Click here
A0A0D2H4M8 View 3D Structure Click here
A0A0K0ENG9 View 3D Structure Click here
A0A0N4UK13 View 3D Structure Click here
A0A0N4UK14 View 3D Structure Click here
A0A175W0F2 View 3D Structure Click here
A0A1C1CSQ4 View 3D Structure Click here
A0A1D6K5Z2 View 3D Structure Click here
A0A1D6KFN9 View 3D Structure Click here
A0A1D6P8K6 View 3D Structure Click here
A0A1D6Q9L1 View 3D Structure Click here
A0A1D6QQM5 View 3D Structure Click here
A0A368UGC3 View 3D Structure Click here
A0A3P7DJY6 View 3D Structure Click here
A0A3Q0KDX8 View 3D Structure Click here
A0A5K4EBN3 View 3D Structure Click here
A4I5D2 View 3D Structure Click here
A5PKG6 View 3D Structure Click here
C0H4Y0 View 3D Structure Click here
C0NIW2 View 3D Structure Click here
E7F6E1 View 3D Structure Click here
E7FEA3 View 3D Structure Click here
E9Q735 View 3D Structure Click here
F1M8V2 View 3D Structure Click here
I1KBB2 View 3D Structure Click here
I1LWP5 View 3D Structure Click here
K7KLL7 View 3D Structure Click here
O44007 View 3D Structure Click here
O95155 View 3D Structure Click here
P54860 View 3D Structure Click here
Q09349 View 3D Structure Click here
Q14139 View 3D Structure Click here
Q4DG09 View 3D Structure Click here
Q4E0T5 View 3D Structure Click here
Q584R0 View 3D Structure Click here
Q5AND8 View 3D Structure Click here
Q5R9G3 View 3D Structure Click here
Q6P7A2 View 3D Structure Click here